The story follows the "strongest juvenile delinquent," Oga Tatsumi, who is a first year at Ishiyama High, a school for delinquents. The story starts as he is telling the story of how he found the baby, to his best friend Furuichi Takayuki. One day while doing laundry by the river (actually, taking revenge on people trying to kill him in his sleep), he sees a man floating down it. He pulls him to shore and the man splits in half revealing a baby boy inside. This boy is the son of the great demon king and Tatsumi has been chosen as the one to raise it along with the baby's maid, Hilda. The story follows his life with the child and at the delinquent school. The early chapters of the manga follow Oga as he attempts to 'pass on' Baby Beel to other students at Ishiyama, (The theory is that if Oga can find someone more evil and stronger than him, Baby Beel will attach to that person instead of Oga), and he eventually meets the Touhoushinki (Ishiyama's strongest four). He first meets Hajime Kanzaki, the first of the Touhoushinki and the closest to dominating the school. After defeating Kanzaki, Oga, who was originally impressed by his attitude, was found to be even more appealing to Beel.

A while after, Oga discovered a symbol on the back of his right hand. Hilda explains that it is the fly king seal more commonly known as the Zebub spell, the family crest of the royal family. The appearance of the seal means that he has officially made a contract with Beel. She also explains that the more evil he is, the more complex the design of the seal will become. Oga attempts to prevent the seal from growing by preventing himself from getting into fights, but eventually has to give up. This is due to Himekawa, the second of the Touhoushinki, capturing Hilda and Furuichi, so he infiltrated Himekawa's base and defeated him by using the zebub blast for the first time. The consequences of using it caused the crest to stretch across his arm, Hilda commented after looking at the crest that the amount of energy used that time would have driven a normal human mad.A trip to the park caused a meeting with a girl called Aoi who was with her brother Kouta, Oga's first words "Please go out with me" created a misunderstanding which stayed within Aoi's heart. Oga told Beel to fight, possibly as a joke, but Kouta accepted the challenge and easily pushed Beel off a bench, it was this event sparked the rivalry between the two babies. A mother in the park eventually reports him to a police, but was defeated him easily after the policeman insulted Oga and Aoi. It is later revealed that Aoi, who was in disguise the whole time, is (in full) Aoi Kunieda, the leader of the Red Tails and another member of the Touhoushinki.

Aoi, who was apparently away from school during the first two events, returned to school to defeat Oga, as she failed to find his name last time, to prevent him from causing any more trouble within the school. But on encounter, she realized that she had already met Oga, but he was unable to recognize her. After he dodged her attacks twice, he notices Beel's interest in Aoi and so says "Please become this kid's mother", that causes another misunderstanding, when it was actually a request for her to replace him as a parent. The fight is postponed, and Hilda soon arrives to give Beel's milk. The MK5, which returns later in the manga, make their debut in the story only to be defeated in a five panel pattern to be used again later in the story. After the fight Beel senses something which turns out to be the last of the Toushinki, Toujou. Oga, however, did not notice.Aoi sees Oga and Hilda's fight with MK5, and believes in the rumours that they are husband and wife. She is challenged by Hilda to a fight so she can test her ability, the fight ends quickly with Hilda deciding that Aoi wasn't on the same level as Oga. At the same time Oga was confronted by Chiaki and Nene. Two female students told Aoi that Oga had injured the two of them, which later turns out to be MK5.

Aoi fights Oga to avenge her two classmates, while Oga was assuming that she wanted to accept the role of becoming Beel's parent. Nene, at the same time, woke up in the infirmary and goes to warn Aoi of MK5's trap, which turns out to be schemed by Miwa. MK5, however, prevents anyone from interrupting Aoi and Oga's fight. Nene was about to get shot, but Natsume appeared and fought with MK5 to allow Nene to tell Aoi. She was unfortunately too late, as Aoi had already seemed to defeated Oga and was just in time for Miwa and Ikari to take over.

Oga suddenly gets back up and defeats Ikari and Miwa easily. It is then shown that Furuichi and Hilda have been watching the whole time. Oga, Furuichi, Hilda and baby Beel went to the beach in search for Toujou to hand baby Beel over to him, not knowing as this was a plot set by Kanzaki and Himekawa for both Toujou and Oga to crush each other. Aoi went to the beach as well to warn Oga about Toujou's strength. Oga and the gang had troubles searching for Toujou and were set in a wild goose chase. Oga decided to write a letter of challenge to Toujou and have Aoi pass it to him. Aoi attempted to tear it but one of Toujou's henchmen found it. They were supposed to meet between the two rocks at 5 pm. Oga was confronted by the MK5 once again but Oga quickly defeated them and arrived late. Toujou left after crushing several motorcycle gangs which inspired Oga to find Toujou. Later, baby Beel starts feeling sick. It appears he came down with a summer cold, Oga's tattoo mysteriously vanishes and later that night he disappears. Hilda kicks Oga out of his house and leaves to find help in the demon world. Oga goes off to find Beel, and eventually he runs into Tojou, who as it turns out has Beel on his back. After a scuffle, Toujou comes out as the victor, and asks Oga to challenge him again sometime. Once Oga gets home, he is in a surprise to find Hilda there waiting for him, with a strange glob demon doctor known as Dr. Furucas and his assistant Lamia. Furucas reveals that the cold is actually Beel's way of coping with a rise of his power, by keeping the energy within himself, and that he cut off the link between him and Oga to protect him. Lamia then injects Oga with a drug that allows him to reestablish the connection with Beel. He then goes to confront Tojou with the aid of the three other Tohoshinki. Once he makes it to Toujou, Beel returns to normal and goes back to Oga. Toujou and Oga then have one final duel in which Oga is victorious, but baby Beel's influx of power causes him to destroy Ishiyama.Due to their school being destroyed, the students of Ishiyama can only go to their sister school, Saint Ishiyama. Initially, they were constantly looked down on.